[2026-06-08T08:51:41] Launching Arriba 2.4.0
[2026-06-08T08:51:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:56] Reading chimeric alignments from 'tih_rna_sample_00602_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11322024)
[2026-06-08T08:59:24] Marking multi-mapping alignments (marked=6884053)
[2026-06-08T08:59:29] Detecting strandedness (reverse)
[2026-06-08T08:59:29] Assigning strands to alignments 
[2026-06-08T08:59:32] Annotating alignments 
[2026-06-08T09:00:19] Filtering duplicates (remaining=7759513)
[2026-06-08T09:00:28] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=7518058)
[2026-06-08T09:00:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7518058)
[2026-06-08T09:00:33] Filtering viral contigs with expression lower than the top 5 (remaining=7518058)
[2026-06-08T09:00:39] Filtering viral contigs with less than 5% coverage (remaining=7518058)
[2026-06-08T09:00:41] Estimating fragment length (mate gap mean=-85.2862, mate gap stddev=31.8627, read length mean=137.834)
[2026-06-08T09:00:42] Filtering read-through fragments with a distance <=10000bp (remaining=7063782)
[2026-06-08T09:00:46] Filtering inconsistently clipped mates (remaining=6972471)
[2026-06-08T09:00:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6800949)
[2026-06-08T09:00:54] Filtering fragments with small insert size (remaining=6800354)
[2026-06-08T09:00:56] Filtering alignments with long gaps (remaining=6800354)
[2026-06-08T09:00:59] Filtering fragments with both mates in the same gene (remaining=6799168)
[2026-06-08T09:01:02] Filtering fusions arising from hairpin structures (remaining=6436152)
[2026-06-08T09:01:05] Filtering reads with a mismatch p-value <=0.01 (remaining=3398997)
[2026-06-08T09:01:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=1160749)
[2026-06-08T09:01:41] Finding fusions and counting supporting reads (total=881383)
[2026-06-08T09:02:01] Merging adjacent fusion breakpoints (remaining=873009)
[2026-06-08T09:02:03] Filtering multi-mapping fusions by alignment score and read support (remaining=574495)
[2026-06-08T09:02:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=571461)
[2026-06-08T09:02:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=306410)
[2026-06-08T09:03:01] Filtering fusions with <2 supporting reads (remaining=45685)
[2026-06-08T09:03:02] Filtering fusions with an e-value >=0.3 (remaining=16997)
[2026-06-08T09:03:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17055)
[2026-06-08T09:03:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16947)
[2026-06-08T09:03:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16947)
[2026-06-08T09:03:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10343)
[2026-06-08T09:03:19] Searching for fusions with spliced split reads (remaining=10375)
[2026-06-08T09:03:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=5147)
[2026-06-08T09:03:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5065)
[2026-06-08T09:03:28] Searching for fusions with >=4 spliced events (remaining=6340)
[2026-06-08T09:03:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2561)
[2026-06-08T09:03:48] Filtering fusions with anchors <=23nt (remaining=2013)
[2026-06-08T09:03:49] Filtering end-to-end fusions with low support (remaining=1967)
[2026-06-08T09:03:50] Filtering fusions with no coverage around the breakpoints (remaining=1923)
[2026-06-08T09:03:51] Indexing gene sequences 
[2026-06-08T09:03:57] Filtering genes with >=30% identity (remaining=462)
[2026-06-08T09:04:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=158)
[2026-06-08T09:04:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T09:04:07] Searching for additional isoforms (remaining=189)
[2026-06-08T09:04:10] Assigning confidence scores to events 
[2026-06-08T09:04:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:16] Writing fusions to file 'tih_rna_sample_00602_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:18] Writing discarded fusions to file 'tih_rna_sample_00602_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:00] Freeing resources
[2026-06-08T09:05:22] Done (elapsed time=00:13:41, CPU time=00:13:39, peak memory=15.8gb)